[{"language":[{"iso":"eng"}],"department":[{"_id":"SaSi"}],"publication":"Journal of Computational Neuroscience","publication_status":"published","publication_identifier":{"eissn":["1573-6873"],"issn":["0929-5313"]},"page":"85-102","ec_funded":1,"author":[{"last_name":"Cubero","id":"850B2E12-9CD4-11E9-837F-E719E6697425","full_name":"Cubero, Ryan J","first_name":"Ryan J","orcid":"0000-0003-0002-1867"},{"last_name":"Marsili","first_name":"Matteo","full_name":"Marsili, Matteo"},{"full_name":"Roudi, Yasser","first_name":"Yasser","last_name":"Roudi"}],"has_accepted_license":"1","intvolume":"        48","keyword":["Time series analysis","Multiple time scale analysis","Spike train data","Information theory","Bayesian decoding"],"publisher":"Springer Nature","abstract":[{"text":"Neuronal responses to complex stimuli and tasks can encompass a wide range of time scales. Understanding these responses requires measures that characterize how the information on these response patterns are represented across multiple temporal resolutions. In this paper we propose a metric – which we call multiscale relevance (MSR) – to capture the dynamical variability of the activity of single neurons across different time scales. The MSR is a non-parametric, fully featureless indicator in that it uses only the time stamps of the firing activity without resorting to any a priori covariate or invoking any specific structure in the tuning curve for neural activity. When applied to neural data from the mEC and from the ADn and PoS regions of freely-behaving rodents, we found that neurons having low MSR tend to have low mutual information and low firing sparsity across the correlates that are believed to be encoded by the region of the brain where the recordings were made. In addition, neurons with high MSR contain significant information on spatial navigation and allow to decode spatial position or head direction as efficiently as those neurons whose firing activity has high mutual information with the covariate to be decoded and significantly better than the set of neurons with high local variations in their interspike intervals. Given these results, we propose that the MSR can be used as a measure to rank and select neurons for their information content without the need to appeal to any a priori covariate.","lang":"eng"}],"date_updated":"2023-08-17T14:35:22Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-02-01T00:00:00Z","file":[{"relation":"supplementary_material","file_id":"7380","checksum":"036e9451d6cd0c190ad25791bf82393b","date_updated":"2020-07-14T12:47:56Z","file_size":1941355,"date_created":"2020-01-28T09:31:09Z","creator":"rcubero","file_name":"10827_2020_740_MOESM1_ESM.pdf","content_type":"application/pdf","access_level":"open_access"},{"creator":"rcubero","date_created":"2020-01-28T09:31:09Z","content_type":"application/pdf","file_name":"Cubero2020_Article_MultiscaleRelevanceAndInformat.pdf","access_level":"open_access","checksum":"4dd8b1fd4b54486f79d82ac7b2a412b2","date_updated":"2020-07-14T12:47:56Z","relation":"main_file","file_id":"7381","file_size":3257880}],"file_date_updated":"2020-07-14T12:47:56Z","scopus_import":"1","month":"02","external_id":{"isi":["000515321800006"]},"acknowledgement":"This research was supported by the Kavli Foundation and the Centre of Excellence scheme of the Research Council of Norway (Centre for Neural Computation). RJC is currently receiving funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","volume":48,"status":"public","isi":1,"date_created":"2020-01-28T10:34:00Z","year":"2020","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","day":"01","_id":"7369","oa":1,"title":"Multiscale relevance and informative encoding in neuronal spike trains","doi":"10.1007/s10827-020-00740-x","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"citation":{"ieee":"R. J. Cubero, M. Marsili, and Y. Roudi, “Multiscale relevance and informative encoding in neuronal spike trains,” <i>Journal of Computational Neuroscience</i>, vol. 48. Springer Nature, pp. 85–102, 2020.","apa":"Cubero, R. J., Marsili, M., &#38; Roudi, Y. (2020). Multiscale relevance and informative encoding in neuronal spike trains. <i>Journal of Computational Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10827-020-00740-x\">https://doi.org/10.1007/s10827-020-00740-x</a>","mla":"Cubero, Ryan J., et al. “Multiscale Relevance and Informative Encoding in Neuronal Spike Trains.” <i>Journal of Computational Neuroscience</i>, vol. 48, Springer Nature, 2020, pp. 85–102, doi:<a href=\"https://doi.org/10.1007/s10827-020-00740-x\">10.1007/s10827-020-00740-x</a>.","short":"R.J. Cubero, M. Marsili, Y. Roudi, Journal of Computational Neuroscience 48 (2020) 85–102.","ama":"Cubero RJ, Marsili M, Roudi Y. Multiscale relevance and informative encoding in neuronal spike trains. <i>Journal of Computational Neuroscience</i>. 2020;48:85-102. doi:<a href=\"https://doi.org/10.1007/s10827-020-00740-x\">10.1007/s10827-020-00740-x</a>","ista":"Cubero RJ, Marsili M, Roudi Y. 2020. Multiscale relevance and informative encoding in neuronal spike trains. Journal of Computational Neuroscience. 48, 85–102.","chicago":"Cubero, Ryan J, Matteo Marsili, and Yasser Roudi. “Multiscale Relevance and Informative Encoding in Neuronal Spike Trains.” <i>Journal of Computational Neuroscience</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s10827-020-00740-x\">https://doi.org/10.1007/s10827-020-00740-x</a>."},"type":"journal_article","ddc":["004","519","570"],"article_processing_charge":"Yes (via OA deal)","article_type":"original"},{"abstract":[{"lang":"eng","text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature."}],"date_updated":"2024-02-21T12:42:31Z","day":"28","file":[{"creator":"rgrah","date_created":"2020-01-28T10:39:40Z","access_level":"open_access","file_name":"Scripts.zip","content_type":"application/zip","date_updated":"2020-07-14T12:47:57Z","checksum":"9d292cf5207b3829225f44c044cdb3fd","file_id":"7384","relation":"main_file","file_size":73363365},{"file_size":962,"checksum":"4076ceab32ef588cc233802bab24c1ab","date_updated":"2020-07-14T12:47:57Z","relation":"main_file","file_id":"7385","content_type":"text/plain","file_name":"READ_ME_MAIN.txt","access_level":"open_access","creator":"rgrah","date_created":"2020-01-28T10:39:30Z"}],"oa":1,"date_published":"2020-01-28T00:00:00Z","_id":"7383","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation.” Institute of Science and Technology Austria, 2020.","apa":"Grah, R. (2020). Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7383\">https://doi.org/10.15479/AT:ISTA:7383</a>","mla":"Grah, Rok. <i>Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7383\">10.15479/AT:ISTA:7383</a>.","short":"R. Grah, (2020).","ama":"Grah R. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7383\">10.15479/AT:ISTA:7383</a>","ista":"Grah R. 2020. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:7383\">10.15479/AT:ISTA:7383</a>.","chicago":"Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7383\">https://doi.org/10.15479/AT:ISTA:7383</a>."},"file_date_updated":"2020-07-14T12:47:57Z","doi":"10.15479/AT:ISTA:7383","title":"Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation","month":"01","article_processing_charge":"No","type":"research_data","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"related_material":{"record":[{"relation":"used_in_publication","id":"7652","status":"public"}]},"status":"public","contributor":[{"contributor_type":"project_leader","orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet"}],"date_created":"2020-01-28T10:41:49Z","has_accepted_license":"1","author":[{"orcid":"0000-0003-2539-3560","first_name":"Rok","full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","last_name":"Grah"}],"publisher":"Institute of Science and Technology Austria","keyword":["Matlab scripts","analysis of microfluidics","mathematical model"],"oa_version":"Published Version","year":"2020"},{"abstract":[{"lang":"eng","text":"Most bacteria accomplish cell division with the help of a dynamic protein complex called the divisome, which spans the cell envelope in the plane of division. Assembly and activation of this machinery are coordinated by the tubulin-related GTPase FtsZ, which was found to form treadmilling filaments on supported bilayers in vitro1, as well as in live cells, in which filaments circle around the cell division site2,3. Treadmilling of FtsZ is thought to actively move proteins around the division septum, thereby distributing peptidoglycan synthesis and coordinating the inward growth of the septum to form the new poles of the daughter cells4. However, the molecular mechanisms underlying this function are largely unknown. Here, to study how FtsZ polymerization dynamics are coupled to downstream proteins, we reconstituted part of the bacterial cell division machinery using its purified components FtsZ, FtsA and truncated transmembrane proteins essential for cell division. We found that the membrane-bound cytosolic peptides of FtsN and FtsQ co-migrated with treadmilling FtsZ–FtsA filaments, but despite their directed collective behaviour, individual peptides showed random motion and transient confinement. Our work suggests that divisome proteins follow treadmilling FtsZ filaments by a diffusion-and-capture mechanism, which can give rise to a moving zone of signalling activity at the division site."}],"date_updated":"2023-10-06T12:22:38Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-01-20T00:00:00Z","scopus_import":"1","month":"01","publication_status":"published","department":[{"_id":"MaLo"}],"language":[{"iso":"eng"}],"publication":"Nature Microbiology","ec_funded":1,"page":"407-417","publication_identifier":{"issn":["2058-5276"]},"author":[{"last_name":"Baranova","full_name":"Baranova, Natalia S.","first_name":"Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124"},{"orcid":"0000-0001-9198-2182 ","last_name":"Radler","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","full_name":"Radler, Philipp","first_name":"Philipp"},{"first_name":"Víctor M.","full_name":"Hernández-Rocamora, Víctor M.","last_name":"Hernández-Rocamora"},{"full_name":"Alfonso, Carlos","first_name":"Carlos","last_name":"Alfonso"},{"last_name":"Lopez Pelegrin","first_name":"Maria D","full_name":"Lopez Pelegrin, Maria D","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rivas","full_name":"Rivas, Germán","first_name":"Germán"},{"full_name":"Vollmer, Waldemar","first_name":"Waldemar","last_name":"Vollmer"},{"orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Springer Nature","intvolume":"         5","quality_controlled":"1","day":"20","oa":1,"_id":"7387","project":[{"grant_number":"679239","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"_id":"259B655A-B435-11E9-9278-68D0E5697425","grant_number":"LT000824/2016","name":"Reconstitution of bacterial cell wall sythesis"},{"_id":"2596EAB6-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 2015-1163","name":"Synthesis of bacterial cell wall"}],"citation":{"short":"N.S. Baranova, P. Radler, V.M. Hernández-Rocamora, C. Alfonso, M.D. Lopez Pelegrin, G. Rivas, W. Vollmer, M. Loose, Nature Microbiology 5 (2020) 407–417.","mla":"Baranova, Natalia S., et al. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” <i>Nature Microbiology</i>, vol. 5, Springer Nature, 2020, pp. 407–17, doi:<a href=\"https://doi.org/10.1038/s41564-019-0657-5\">10.1038/s41564-019-0657-5</a>.","apa":"Baranova, N. S., Radler, P., Hernández-Rocamora, V. M., Alfonso, C., Lopez Pelegrin, M. D., Rivas, G., … Loose, M. (2020). Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. <i>Nature Microbiology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41564-019-0657-5\">https://doi.org/10.1038/s41564-019-0657-5</a>","ama":"Baranova NS, Radler P, Hernández-Rocamora VM, et al. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. <i>Nature Microbiology</i>. 2020;5:407-417. doi:<a href=\"https://doi.org/10.1038/s41564-019-0657-5\">10.1038/s41564-019-0657-5</a>","ista":"Baranova NS, Radler P, Hernández-Rocamora VM, Alfonso C, Lopez Pelegrin MD, Rivas G, Vollmer W, Loose M. 2020. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 5, 407–417.","chicago":"Baranova, Natalia S., Philipp Radler, Víctor M. Hernández-Rocamora, Carlos Alfonso, Maria D Lopez Pelegrin, Germán Rivas, Waldemar Vollmer, and Martin Loose. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” <i>Nature Microbiology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41564-019-0657-5\">https://doi.org/10.1038/s41564-019-0657-5</a>.","ieee":"N. S. Baranova <i>et al.</i>, “Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins,” <i>Nature Microbiology</i>, vol. 5. Springer Nature, pp. 407–417, 2020."},"pmid":1,"doi":"10.1038/s41564-019-0657-5","title":"Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins","article_processing_charge":"No","article_type":"letter_note","type":"journal_article","external_id":{"pmid":["31959972"],"isi":["000508584700007"]},"related_material":{"record":[{"id":"14280","status":"public","relation":"dissertation_contains"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/little-cell-big-cover-story/","relation":"press_release"}]},"acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular, P. Caldas for help with the treadmilling analysis, M. Jimenez, A. Raso and N. Ropero for providing Alexa Fluor 488- and Alexa Fluor 647-labelled FtsA for the MST and analytical ultracentrifugation experiments. We thank C. You for providing the DODA-tris-NTA phospholipids, as well as J. Piehler and C. Richter (Department of Biology, University of Osnabruck, Germany) for the SLIMfast single-molecule tracking software and help with the confinement analysis. We thank J. Errington and H. Murray (both at Newcastle University, UK) for critical reading of the manuscript, and J. Brugués (MPI-CBG and MPI-PKS, Dresden, Germany) for help with the MATLAB programming and reading of the manuscript. This work was supported by the European Research Council through grant ERC-2015-StG-679239 to M.L. and grants HFSP LT 000824/2016-L4 and EMBO ALTF 1163-2015 to N.B., a grant from the Ministry of Economy and Competitiveness of the Spanish Government (BFU2016-75471-C2-1-P) to C.A. and G.R., and a Wellcome Trust Senior Investigator award (101824/Z/13/Z) and a grant from the BBSRC (BB/R017409/1) to W.V.","volume":5,"status":"public","date_created":"2020-01-28T16:14:41Z","isi":1,"oa_version":"Submitted Version","main_file_link":[{"url":"http://europepmc.org/article/PMC/7048620","open_access":"1"}],"year":"2020"},{"scopus_import":"1","month":"05","abstract":[{"text":"We give a Wong-Zakai type characterisation of the solutions of quasilinear heat equations driven by space-time white noise in 1 + 1 dimensions. In order to show that the renormalisation counterterms are local in the solution, a careful arrangement of a few hundred terms is required. The main tool in this computation is a general ‘integration by parts’ formula that provides a number of linear identities for the renormalisation constants.","lang":"eng"}],"date_updated":"2023-08-17T14:35:46Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-05-01T00:00:00Z","author":[{"first_name":"Mate","full_name":"Gerencser, Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Gerencser"}],"publisher":"Elsevier","intvolume":"        37","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"JaMa"}],"publication":"Annales de l'Institut Henri Poincaré C, Analyse non linéaire","page":"663-682","publication_identifier":{"issn":["0294-1449"]},"citation":{"ama":"Gerencser M. Nondivergence form quasilinear heat equations driven by space-time white noise. <i>Annales de l’Institut Henri Poincaré C, Analyse non linéaire</i>. 2020;37(3):663-682. doi:<a href=\"https://doi.org/10.1016/j.anihpc.2020.01.003\">10.1016/j.anihpc.2020.01.003</a>","chicago":"Gerencser, Mate. “Nondivergence Form Quasilinear Heat Equations Driven by Space-Time White Noise.” <i>Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.anihpc.2020.01.003\">https://doi.org/10.1016/j.anihpc.2020.01.003</a>.","ista":"Gerencser M. 2020. Nondivergence form quasilinear heat equations driven by space-time white noise. Annales de l’Institut Henri Poincaré C, Analyse non linéaire. 37(3), 663–682.","short":"M. Gerencser, Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire 37 (2020) 663–682.","mla":"Gerencser, Mate. “Nondivergence Form Quasilinear Heat Equations Driven by Space-Time White Noise.” <i>Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire</i>, vol. 37, no. 3, Elsevier, 2020, pp. 663–82, doi:<a href=\"https://doi.org/10.1016/j.anihpc.2020.01.003\">10.1016/j.anihpc.2020.01.003</a>.","apa":"Gerencser, M. (2020). Nondivergence form quasilinear heat equations driven by space-time white noise. <i>Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.anihpc.2020.01.003\">https://doi.org/10.1016/j.anihpc.2020.01.003</a>","ieee":"M. Gerencser, “Nondivergence form quasilinear heat equations driven by space-time white noise,” <i>Annales de l’Institut Henri Poincaré C, Analyse non linéaire</i>, vol. 37, no. 3. Elsevier, pp. 663–682, 2020."},"doi":"10.1016/j.anihpc.2020.01.003","title":"Nondivergence form quasilinear heat equations driven by space-time white noise","article_processing_charge":"No","article_type":"original","type":"journal_article","quality_controlled":"1","day":"01","oa":1,"_id":"7388","date_created":"2020-01-29T09:39:41Z","isi":1,"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1902.07635","open_access":"1"}],"year":"2020","external_id":{"isi":["000531049800007"],"arxiv":["1902.07635"]},"issue":"3","arxiv":1,"volume":37,"status":"public"},{"arxiv":1,"status":"public","volume":373,"external_id":{"isi":["000551418100018"],"arxiv":["2002.00859"]},"issue":"8","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/2002.00859","open_access":"1"}],"year":"2020","date_created":"2020-01-29T10:20:46Z","isi":1,"oa":1,"_id":"7389","day":"01","quality_controlled":"1","article_type":"original","article_processing_charge":"No","ddc":["515"],"type":"journal_article","citation":{"short":"G.P. Geher, T. Titkos, D. Virosztek, Transactions of the American Mathematical Society 373 (2020) 5855–5883.","apa":"Geher, G. P., Titkos, T., &#38; Virosztek, D. (2020). Isometric study of Wasserstein spaces - the real line. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/8113\">https://doi.org/10.1090/tran/8113</a>","mla":"Geher, Gyorgy Pal, et al. “Isometric Study of Wasserstein Spaces - the Real Line.” <i>Transactions of the American Mathematical Society</i>, vol. 373, no. 8, American Mathematical Society, 2020, pp. 5855–83, doi:<a href=\"https://doi.org/10.1090/tran/8113\">10.1090/tran/8113</a>.","ista":"Geher GP, Titkos T, Virosztek D. 2020. Isometric study of Wasserstein spaces - the real line. Transactions of the American Mathematical Society. 373(8), 5855–5883.","chicago":"Geher, Gyorgy Pal, Tamas Titkos, and Daniel Virosztek. “Isometric Study of Wasserstein Spaces - the Real Line.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2020. <a href=\"https://doi.org/10.1090/tran/8113\">https://doi.org/10.1090/tran/8113</a>.","ama":"Geher GP, Titkos T, Virosztek D. Isometric study of Wasserstein spaces - the real line. <i>Transactions of the American Mathematical Society</i>. 2020;373(8):5855-5883. doi:<a href=\"https://doi.org/10.1090/tran/8113\">10.1090/tran/8113</a>","ieee":"G. P. Geher, T. Titkos, and D. Virosztek, “Isometric study of Wasserstein spaces - the real line,” <i>Transactions of the American Mathematical Society</i>, vol. 373, no. 8. American Mathematical Society, pp. 5855–5883, 2020."},"project":[{"call_identifier":"H2020","grant_number":"846294","name":"Geometric study of Wasserstein spaces and free probability","_id":"26A455A6-B435-11E9-9278-68D0E5697425"}],"title":"Isometric study of Wasserstein spaces - the real line","doi":"10.1090/tran/8113","ec_funded":1,"page":"5855-5883","publication_identifier":{"eissn":["10886850"],"issn":["00029947"]},"publication_status":"published","publication":"Transactions of the American Mathematical Society","language":[{"iso":"eng"}],"department":[{"_id":"LaEr"}],"publisher":"American Mathematical Society","keyword":["Wasserstein space","isometric embeddings","isometric rigidity","exotic isometry flow"],"intvolume":"       373","author":[{"last_name":"Geher","full_name":"Geher, Gyorgy Pal","first_name":"Gyorgy Pal"},{"last_name":"Titkos","first_name":"Tamas","full_name":"Titkos, Tamas"},{"id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","full_name":"Virosztek, Daniel","last_name":"Virosztek","orcid":"0000-0003-1109-5511"}],"date_published":"2020-08-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Recently Kloeckner described the structure of the isometry group of the quadratic Wasserstein space W_2(R^n). It turned out that the case of the real line is exceptional in the sense that there exists an exotic isometry flow. Following this line of investigation, we compute Isom(W_p(R)), the isometry group of the Wasserstein space\r\nW_p(R) for all p \\in [1,\\infty) \\setminus {2}. We show that W_2(R) is also exceptional regarding the\r\nparameter p: W_p(R) is isometrically rigid if and only if p is not equal to 2. Regarding the underlying\r\nspace, we prove that the exceptionality of p = 2 disappears if we replace R by the compact\r\ninterval [0,1]. Surprisingly, in that case, W_p([0,1]) is isometrically rigid if and only if\r\np is not equal to 1. Moreover, W_1([0,1]) admits isometries that split mass, and Isom(W_1([0,1]))\r\ncannot be embedded into Isom(W_1(R)).","lang":"eng"}],"date_updated":"2023-08-17T14:31:03Z","month":"08"},{"external_id":{"arxiv":["1808.07350"],"isi":["000557689300003"]},"volume":2256,"status":"public","arxiv":1,"isi":1,"date_created":"2018-12-11T11:44:29Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.07350"}],"year":"2020","oa_version":"Preprint","day":"21","quality_controlled":"1","editor":[{"first_name":"Bo'az","full_name":"Klartag, Bo'az","last_name":"Klartag"},{"last_name":"Milman","first_name":"Emanuel","full_name":"Milman, Emanuel"}],"_id":"74","oa":1,"title":"Gromov's waist of non-radial Gaussian measures and radial non-Gaussian measures","doi":"10.1007/978-3-030-36020-7_1","citation":{"ieee":"A. Akopyan and R. Karasev, “Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures,” in <i>Geometric Aspects of Functional Analysis</i>, vol. 2256, B. Klartag and E. Milman, Eds. Springer Nature, 2020, pp. 1–27.","short":"A. Akopyan, R. Karasev, in:, B. Klartag, E. Milman (Eds.), Geometric Aspects of Functional Analysis, Springer Nature, 2020, pp. 1–27.","apa":"Akopyan, A., &#38; Karasev, R. (2020). Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures. In B. Klartag &#38; E. Milman (Eds.), <i>Geometric Aspects of Functional Analysis</i> (Vol. 2256, pp. 1–27). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-36020-7_1\">https://doi.org/10.1007/978-3-030-36020-7_1</a>","mla":"Akopyan, Arseniy, and Roman Karasev. “Gromov’s Waist of Non-Radial Gaussian Measures and Radial Non-Gaussian Measures.” <i>Geometric Aspects of Functional Analysis</i>, edited by Bo’az Klartag and Emanuel Milman, vol. 2256, Springer Nature, 2020, pp. 1–27, doi:<a href=\"https://doi.org/10.1007/978-3-030-36020-7_1\">10.1007/978-3-030-36020-7_1</a>.","ama":"Akopyan A, Karasev R. Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures. In: Klartag B, Milman E, eds. <i>Geometric Aspects of Functional Analysis</i>. Vol 2256. LNM. Springer Nature; 2020:1-27. doi:<a href=\"https://doi.org/10.1007/978-3-030-36020-7_1\">10.1007/978-3-030-36020-7_1</a>","chicago":"Akopyan, Arseniy, and Roman Karasev. “Gromov’s Waist of Non-Radial Gaussian Measures and Radial Non-Gaussian Measures.” In <i>Geometric Aspects of Functional Analysis</i>, edited by Bo’az Klartag and Emanuel Milman, 2256:1–27. LNM. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-36020-7_1\">https://doi.org/10.1007/978-3-030-36020-7_1</a>.","ista":"Akopyan A, Karasev R. 2020.Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures. In: Geometric Aspects of Functional Analysis. vol. 2256, 1–27."},"project":[{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425"}],"type":"book_chapter","article_processing_charge":"No","publication":"Geometric Aspects of Functional Analysis","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"},{"_id":"JaMa"}],"publication_status":"published","publication_identifier":{"issn":["00758434"],"eissn":["16179692"],"isbn":["9783030360191"],"eisbn":["9783030360207"]},"page":"1-27","ec_funded":1,"author":[{"orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy","first_name":"Arseniy","last_name":"Akopyan"},{"first_name":"Roman","full_name":"Karasev, Roman","last_name":"Karasev"}],"intvolume":"      2256","publisher":"Springer Nature","abstract":[{"lang":"eng","text":"We study the Gromov waist in the sense of t-neighborhoods for measures in the Euclidean  space,  motivated  by  the  famous  theorem  of  Gromov  about  the  waist  of  radially symmetric Gaussian measures.  In particular, it turns our possible to extend Gromov’s original result  to  the  case  of  not  necessarily  radially  symmetric  Gaussian  measure.   We  also  provide examples of measures having no t-neighborhood waist property, including a rather wide class\r\nof compactly supported radially symmetric measures and their maps into the Euclidean space of dimension at least 2.\r\nWe  use  a  simpler  form  of  Gromov’s  pancake  argument  to  produce  some  estimates  of t-neighborhoods of (weighted) volume-critical submanifolds in the spirit of the waist theorems, including neighborhoods of algebraic manifolds in the complex projective space. In the appendix of this paper we provide for reader’s convenience a more detailed explanation of the Caffarelli theorem that we use to handle not necessarily radially symmetric Gaussian\r\nmeasures."}],"date_updated":"2023-08-17T13:48:31Z","date_published":"2020-06-21T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","series_title":"LNM","month":"06"},{"abstract":[{"lang":"eng","text":"Epiboly is a conserved gastrulation movement describing the thinning and spreading of a sheet or multi-layer of cells. The zebrafish embryo has emerged as a vital model system to address the cellular and molecular mechanisms that drive epiboly. In the zebrafish embryo, the blastoderm, consisting of a simple squamous epithelium (the enveloping layer) and an underlying mass of deep cells, as well as a yolk nuclear syncytium (the yolk syncytial layer) undergo epiboly to internalize the yolk cell during gastrulation. The major events during zebrafish epiboly are: expansion of the enveloping layer and the internal yolk syncytial layer, reduction and removal of the yolk membrane ahead of the advancing blastoderm margin and deep cell rearrangements between the enveloping layer and yolk syncytial layer to thin the blastoderm. Here, work addressing the cellular and molecular mechanisms as well as the sources of the mechanical forces that underlie these events is reviewed. The contribution of recent findings to the current model of epiboly as well as open questions and future prospects are also discussed."}],"date_updated":"2024-02-22T13:23:09Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2020-01-01T00:00:00Z","scopus_import":"1","month":"01","series_title":"Current Topics in Developmental Biology","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"CaHe"}],"publication":"Gastrulation: From Embryonic Pattern to Form","page":"319-341","publication_identifier":{"isbn":["9780128127988"],"issn":["0070-2153"]},"author":[{"full_name":"Bruce, Ashley E.E.","first_name":"Ashley E.E.","last_name":"Bruce"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Elsevier","intvolume":"       136","quality_controlled":"1","day":"01","_id":"7410","editor":[{"first_name":"Lilianna ","full_name":"Solnica-Krezel, Lilianna ","last_name":"Solnica-Krezel"}],"citation":{"ieee":"A. E. E. Bruce and C.-P. J. Heisenberg, “Mechanisms of zebrafish epiboly: A current view,” in <i>Gastrulation: From Embryonic Pattern to Form</i>, vol. 136, L. Solnica-Krezel, Ed. Elsevier, 2020, pp. 319–341.","short":"A.E.E. Bruce, C.-P.J. Heisenberg, in:, L. Solnica-Krezel (Ed.), Gastrulation: From Embryonic Pattern to Form, Elsevier, 2020, pp. 319–341.","mla":"Bruce, Ashley E. E., and Carl-Philipp J. Heisenberg. “Mechanisms of Zebrafish Epiboly: A Current View.” <i>Gastrulation: From Embryonic Pattern to Form</i>, edited by Lilianna  Solnica-Krezel, vol. 136, Elsevier, 2020, pp. 319–41, doi:<a href=\"https://doi.org/10.1016/bs.ctdb.2019.07.001\">10.1016/bs.ctdb.2019.07.001</a>.","apa":"Bruce, A. E. E., &#38; Heisenberg, C.-P. J. (2020). Mechanisms of zebrafish epiboly: A current view. In L. Solnica-Krezel (Ed.), <i>Gastrulation: From Embryonic Pattern to Form</i> (Vol. 136, pp. 319–341). Elsevier. <a href=\"https://doi.org/10.1016/bs.ctdb.2019.07.001\">https://doi.org/10.1016/bs.ctdb.2019.07.001</a>","ama":"Bruce AEE, Heisenberg C-PJ. Mechanisms of zebrafish epiboly: A current view. In: Solnica-Krezel L, ed. <i>Gastrulation: From Embryonic Pattern to Form</i>. Vol 136. Current Topics in Developmental Biology. Elsevier; 2020:319-341. doi:<a href=\"https://doi.org/10.1016/bs.ctdb.2019.07.001\">10.1016/bs.ctdb.2019.07.001</a>","ista":"Bruce AEE, Heisenberg C-PJ. 2020.Mechanisms of zebrafish epiboly: A current view. In: Gastrulation: From Embryonic Pattern to Form. vol. 136, 319–341.","chicago":"Bruce, Ashley E.E., and Carl-Philipp J Heisenberg. “Mechanisms of Zebrafish Epiboly: A Current View.” In <i>Gastrulation: From Embryonic Pattern to Form</i>, edited by Lilianna  Solnica-Krezel, 136:319–41. Current Topics in Developmental Biology. Elsevier, 2020. <a href=\"https://doi.org/10.1016/bs.ctdb.2019.07.001\">https://doi.org/10.1016/bs.ctdb.2019.07.001</a>."},"doi":"10.1016/bs.ctdb.2019.07.001","title":"Mechanisms of zebrafish epiboly: A current view","article_processing_charge":"No","type":"book_chapter","external_id":{"isi":["000611830600012"]},"volume":136,"status":"public","date_created":"2020-01-30T09:24:06Z","isi":1,"oa_version":"None","year":"2020"},{"day":"01","quality_controlled":"1","_id":"7416","oa":1,"pmid":1,"title":"Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation","doi":"10.1080/15592324.2019.1687175","citation":{"ista":"Sinclair SA, Krämer U. 2020. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling &#38; Behavior. 15(1), 1687175.","chicago":"Sinclair, Scott A, and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis, 2020. <a href=\"https://doi.org/10.1080/15592324.2019.1687175\">https://doi.org/10.1080/15592324.2019.1687175</a>.","ama":"Sinclair SA, Krämer U. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. <i>Plant Signaling &#38; Behavior</i>. 2020;15(1). doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687175\">10.1080/15592324.2019.1687175</a>","short":"S.A. Sinclair, U. Krämer, Plant Signaling &#38; Behavior 15 (2020).","mla":"Sinclair, Scott A., and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1, 1687175, Taylor &#38; Francis, 2020, doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687175\">10.1080/15592324.2019.1687175</a>.","apa":"Sinclair, S. A., &#38; Krämer, U. (2020). Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/15592324.2019.1687175\">https://doi.org/10.1080/15592324.2019.1687175</a>","ieee":"S. A. Sinclair and U. Krämer, “Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation,” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1. Taylor &#38; Francis, 2020."},"type":"journal_article","article_type":"original","article_processing_charge":"No","issue":"1","external_id":{"isi":["000494909300001"],"pmid":["31696764"]},"status":"public","volume":15,"article_number":"1687175","isi":1,"date_created":"2020-01-30T10:12:04Z","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012054"}],"year":"2020","oa_version":"Submitted Version","date_updated":"2023-10-17T09:01:48Z","abstract":[{"text":"Earlier, we demonstrated that transcript levels of METAL TOLERANCE PROTEIN2 (MTP2) and of HEAVY METAL ATPase2 (HMA2) increase strongly in roots of Arabidopsis upon prolonged zinc (Zn) deficiency and respond to shoot physiological Zn status, and not to the local Zn status in roots. This provided evidence for shoot-to-root communication in the acclimation of plants to Zn deficiency. Zn-deficient soils limit both the yield and quality of agricultural crops and can result in clinically relevant nutritional Zn deficiency in human populations. Implementing Zn deficiency during cultivation of the model plant Arabidopsis thaliana on agar-solidified media is difficult because trace element contaminations are present in almost all commercially available agars. Here, we demonstrate root morphological acclimations to Zn deficiency on agar-solidified medium following the effective removal of contaminants. These advancements allow reproducible phenotyping toward understanding fundamental plant responses to deficiencies of Zn and other essential trace elements.","lang":"eng"}],"date_published":"2020-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","month":"01","publication":"Plant Signaling & Behavior","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1559-2324"]},"author":[{"id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","full_name":"Sinclair, Scott A","first_name":"Scott A","last_name":"Sinclair","orcid":"0000-0002-4566-0593"},{"first_name":"U.","full_name":"Krämer, U.","last_name":"Krämer"}],"intvolume":"        15","publisher":"Taylor & Francis"},{"article_number":"e1687185","volume":15,"status":"public","external_id":{"pmid":["31696770"],"isi":["000494907500001"]},"issue":"1","oa_version":"Submitted Version","year":"2020","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012154","open_access":"1"}],"date_created":"2020-01-30T10:14:14Z","isi":1,"oa":1,"_id":"7417","day":"01","quality_controlled":"1","article_type":"original","article_processing_charge":"No","type":"journal_article","citation":{"chicago":"Sinclair, Scott A, S. Gille, M. Pauly, and U. Krämer. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” <i>Plant Signaling &#38; Behavior</i>. Informa UK Limited, 2020. <a href=\"https://doi.org/10.1080/15592324.2019.1687185\">https://doi.org/10.1080/15592324.2019.1687185</a>.","ista":"Sinclair SA, Gille S, Pauly M, Krämer U. 2020. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling &#38; Behavior. 15(1), e1687185.","ama":"Sinclair SA, Gille S, Pauly M, Krämer U. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. <i>Plant Signaling &#38; Behavior</i>. 2020;15(1). doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687185\">10.1080/15592324.2019.1687185</a>","short":"S.A. Sinclair, S. Gille, M. Pauly, U. Krämer, Plant Signaling &#38; Behavior 15 (2020).","apa":"Sinclair, S. A., Gille, S., Pauly, M., &#38; Krämer, U. (2020). Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. <i>Plant Signaling &#38; Behavior</i>. Informa UK Limited. <a href=\"https://doi.org/10.1080/15592324.2019.1687185\">https://doi.org/10.1080/15592324.2019.1687185</a>","mla":"Sinclair, Scott A., et al. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1, e1687185, Informa UK Limited, 2020, doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687185\">10.1080/15592324.2019.1687185</a>.","ieee":"S. A. Sinclair, S. Gille, M. Pauly, and U. Krämer, “Regulation of acetylation of plant cell wall components is complex and responds to external stimuli,” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1. Informa UK Limited, 2020."},"title":"Regulation of acetylation of plant cell wall components is complex and responds to external stimuli","pmid":1,"doi":"10.1080/15592324.2019.1687185","publication_identifier":{"issn":["1559-2324"]},"publication_status":"published","publication":"Plant Signaling & Behavior","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"publisher":"Informa UK Limited","intvolume":"        15","author":[{"first_name":"Scott A","full_name":"Sinclair, Scott A","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","last_name":"Sinclair","orcid":"0000-0002-4566-0593"},{"last_name":"Gille","full_name":"Gille, S.","first_name":"S."},{"first_name":"M.","full_name":"Pauly, M.","last_name":"Pauly"},{"last_name":"Krämer","full_name":"Krämer, U.","first_name":"U."}],"date_published":"2020-01-01T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-06T15:23:04Z","abstract":[{"lang":"eng","text":"Previously, we reported that the allelic de-etiolated by zinc (dez) and trichome birefringence (tbr) mutants exhibit photomorphogenic development in the dark, which is enhanced by high Zn. TRICHOME BIREFRINGENCE-LIKE proteins had been implicated in transferring acetyl groups to various hemicelluloses. Pectin O-acetylation levels were lower in dark-grown dez seedlings than in the wild type. We observed Zn-enhanced photomorphogenesis in the dark also in the reduced wall acetylation 2 (rwa2-3) mutant, which exhibits lowered O-acetylation levels of cell wall macromolecules including pectins and xyloglucans, supporting a role for cell wall macromolecule O-acetylation in the photomorphogenic phenotypes of rwa2-3 and dez. Application of very short oligogalacturonides (vsOGs) restored skotomorphogenesis in dark-grown dez and rwa2-3. Here we demonstrate that in dez, O-acetylation of non-pectin cell wall components, notably of xyloglucan, is enhanced. Our results highlight the complexity of cell wall homeostasis and indicate against an influence of xyloglucan O-acetylation on light-dependent seedling development."}],"month":"01","scopus_import":"1"},{"file_date_updated":"2022-05-16T22:30:04Z","scopus_import":"1","month":"05","date_updated":"2023-08-17T14:32:54Z","abstract":[{"lang":"eng","text":"This paper presents a novel abstraction technique for analyzing Lyapunov and asymptotic stability of polyhedral switched systems. A polyhedral switched system is a hybrid system in which the continuous dynamics is specified by polyhedral differential inclusions, the invariants and guards are specified by polyhedral sets and the switching between the modes do not involve reset of variables. A finite state weighted graph abstracting the polyhedral switched system is constructed from a finite partition of the state–space, such that the satisfaction of certain graph conditions, such as the absence of cycles with product of weights on the edges greater than (or equal) to 1, implies the stability of the system. However, the graph is in general conservative and hence, the violation of the graph conditions does not imply instability. If the analysis fails to establish stability due to the conservativeness in the approximation, a counterexample (cycle with product of edge weights greater than or equal to 1) indicating a potential reason for the failure is returned. Further, a more precise approximation of the switched system can be constructed by considering a finer partition of the state–space in the construction of the finite weighted graph. We present experimental results on analyzing stability of switched systems using the above method."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-05-01T00:00:00Z","file":[{"access_level":"open_access","file_name":"2020_NAHS_GarciaSoto.pdf","content_type":"application/pdf","date_created":"2020-10-21T13:16:45Z","creator":"dernst","embargo":"2022-05-15","file_size":818774,"file_id":"8688","relation":"main_file","date_updated":"2022-05-16T22:30:04Z","checksum":"560abfddb53f9fe921b6744f59f2cfaa"}],"author":[{"orcid":"0000−0003−2936−5719","full_name":"Garcia Soto, Miriam","first_name":"Miriam","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","last_name":"Garcia Soto"},{"full_name":"Prabhakar, Pavithra","first_name":"Pavithra","last_name":"Prabhakar"}],"has_accepted_license":"1","intvolume":"        36","publisher":"Elsevier","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"publication":"Nonlinear Analysis: Hybrid Systems","publication_status":"published","publication_identifier":{"issn":["1751-570X"]},"doi":"10.1016/j.nahs.2020.100856","title":"Abstraction based verification of stability of polyhedral switched systems","project":[{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"M. Garcia Soto, P. Prabhakar, Nonlinear Analysis: Hybrid Systems 36 (2020).","mla":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification of Stability of Polyhedral Switched Systems.” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 36, no. 5, 100856, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.nahs.2020.100856\">10.1016/j.nahs.2020.100856</a>.","apa":"Garcia Soto, M., &#38; Prabhakar, P. (2020). Abstraction based verification of stability of polyhedral switched systems. <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nahs.2020.100856\">https://doi.org/10.1016/j.nahs.2020.100856</a>","ama":"Garcia Soto M, Prabhakar P. Abstraction based verification of stability of polyhedral switched systems. <i>Nonlinear Analysis: Hybrid Systems</i>. 2020;36(5). doi:<a href=\"https://doi.org/10.1016/j.nahs.2020.100856\">10.1016/j.nahs.2020.100856</a>","ista":"Garcia Soto M, Prabhakar P. 2020. Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 36(5), 100856.","chicago":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification of Stability of Polyhedral Switched Systems.” <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.nahs.2020.100856\">https://doi.org/10.1016/j.nahs.2020.100856</a>.","ieee":"M. Garcia Soto and P. Prabhakar, “Abstraction based verification of stability of polyhedral switched systems,” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 36, no. 5. Elsevier, 2020."},"ddc":["000"],"type":"journal_article","article_processing_charge":"No","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"quality_controlled":"1","day":"01","_id":"7426","oa":1,"isi":1,"date_created":"2020-02-02T23:00:59Z","year":"2020","oa_version":"Submitted Version","issue":"5","external_id":{"isi":["000528828600003"]},"status":"public","volume":36,"article_number":"100856"},{"month":"02","file_date_updated":"2020-09-22T09:51:28Z","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-02-03T00:00:00Z","file":[{"date_created":"2020-09-22T09:51:28Z","success":1,"creator":"dernst","access_level":"open_access","content_type":"application/pdf","file_name":"2020_CurrentBiology_Tan.pdf","file_id":"8555","relation":"main_file","date_updated":"2020-09-22T09:51:28Z","checksum":"16f7d51fe28f91c21e4896a2028df40b","file_size":5360135}],"abstract":[{"text":"Plants, like other multicellular organisms, survive through a delicate balance between growth and defense against pathogens. Salicylic acid (SA) is a major defense signal in plants, and the perception mechanism as well as downstream signaling activating the immune response are known. Here, we identify a parallel SA signaling that mediates growth attenuation. SA directly binds to A subunits of protein phosphatase 2A (PP2A), inhibiting activity of this complex. Among PP2A targets, the PIN2 auxin transporter is hyperphosphorylated in response to SA, leading to changed activity of this important growth regulator. Accordingly, auxin transport and auxin-mediated root development, including growth, gravitropic response, and lateral root organogenesis, are inhibited. This study reveals how SA, besides activating immunity, concomitantly attenuates growth through crosstalk with the auxin distribution network. Further analysis of this dual role of SA and characterization of additional SA-regulated PP2A targets will provide further insights into mechanisms maintaining a balance between growth and defense.","lang":"eng"}],"date_updated":"2024-03-25T23:30:20Z","intvolume":"        30","publisher":"Cell Press","has_accepted_license":"1","author":[{"orcid":"0000-0002-0471-8285","last_name":"Tan","full_name":"Tan, Shutang","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Abas","id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","full_name":"Abas, Melinda F","first_name":"Melinda F"},{"orcid":"0000-0001-7241-2328","last_name":"Verstraeten","full_name":"Verstraeten, Inge","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","full_name":"Glanc, Matous","first_name":"Matous","last_name":"Glanc"},{"full_name":"Molnar, Gergely","first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","last_name":"Molnar"},{"orcid":"0000-0003-2140-7195","last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub","first_name":"Jakub"},{"last_name":"Lasák","full_name":"Lasák, Pavel","first_name":"Pavel"},{"full_name":"Petřík, Ivan","first_name":"Ivan","last_name":"Petřík"},{"full_name":"Russinova, Eugenia","first_name":"Eugenia","last_name":"Russinova"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"last_name":"Novák","full_name":"Novák, Ondřej","first_name":"Ondřej"},{"last_name":"Pospíšil","first_name":"Jiří","full_name":"Pospíšil, Jiří"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"publication_identifier":{"issn":["09609822"]},"page":"381-395.e8","ec_funded":1,"language":[{"iso":"eng"}],"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publication":"Current Biology","publication_status":"published","ddc":["580"],"type":"journal_article","article_processing_charge":"No","article_type":"original","doi":"10.1016/j.cub.2019.11.058","title":"Salicylic acid targets protein phosphatase 2A to attenuate growth in plants","pmid":1,"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"256FEF10-B435-11E9-9278-68D0E5697425","grant_number":"723-2015","name":"Long Term Fellowship"}],"citation":{"ieee":"S. Tan <i>et al.</i>, “Salicylic acid targets protein phosphatase 2A to attenuate growth in plants,” <i>Current Biology</i>, vol. 30, no. 3. Cell Press, p. 381–395.e8, 2020.","short":"S. Tan, M.F. Abas, I. Verstraeten, M. Glanc, G. Molnar, J. Hajny, P. Lasák, I. Petřík, E. Russinova, J. Petrášek, O. Novák, J. Pospíšil, J. Friml, Current Biology 30 (2020) 381–395.e8.","apa":"Tan, S., Abas, M. F., Verstraeten, I., Glanc, M., Molnar, G., Hajny, J., … Friml, J. (2020). Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2019.11.058\">https://doi.org/10.1016/j.cub.2019.11.058</a>","mla":"Tan, Shutang, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate Growth in Plants.” <i>Current Biology</i>, vol. 30, no. 3, Cell Press, 2020, p. 381–395.e8, doi:<a href=\"https://doi.org/10.1016/j.cub.2019.11.058\">10.1016/j.cub.2019.11.058</a>.","ama":"Tan S, Abas MF, Verstraeten I, et al. Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. <i>Current Biology</i>. 2020;30(3):381-395.e8. doi:<a href=\"https://doi.org/10.1016/j.cub.2019.11.058\">10.1016/j.cub.2019.11.058</a>","ista":"Tan S, Abas MF, Verstraeten I, Glanc M, Molnar G, Hajny J, Lasák P, Petřík I, Russinova E, Petrášek J, Novák O, Pospíšil J, Friml J. 2020. Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. 30(3), 381–395.e8.","chicago":"Tan, Shutang, Melinda F Abas, Inge Verstraeten, Matous Glanc, Gergely Molnar, Jakub Hajny, Pavel Lasák, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate Growth in Plants.” <i>Current Biology</i>. Cell Press, 2020. <a href=\"https://doi.org/10.1016/j.cub.2019.11.058\">https://doi.org/10.1016/j.cub.2019.11.058</a>."},"_id":"7427","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","day":"03","year":"2020","oa_version":"Published Version","isi":1,"date_created":"2020-02-02T23:01:00Z","acknowledgement":"We thank Shigeyuki Betsuyaku (University of Tsukuba), Alison Delong (Brown University), Xinnian Dong (Duke University), Dolf Weijers (Wageningen University), Yuelin Zhang (UBC), and Martine Pastuglia (Institut Jean-Pierre Bourgin) for sharing published materials; Jana Riederer for help with cantharidin physiological analysis; David Domjan for help with cloning pET28a-PIN2HL; Qing Lu for help with DARTS; Hana Kozubı´kova´ for technical support on SA derivative synthesis; Zuzana Vondra´ kova´ for technical support with tobacco cells; Lucia Strader (Washington University), Bert De Rybel (Ghent University), Bartel Vanholme (Ghent University), and Lukas Mach (BOKU) for helpful discussions; and bioimaging and life science facilities of IST Austria for continuous support. We gratefully acknowledge the Nottingham Arabidopsis Stock Center (NASC) for providing T-DNA insertional mutants. The DSC and SPR instruments were provided by the EQ-BOKU VIBT GmbH and the BOKU Core Facility for Biomolecular and Cellular Analysis, with help of Irene Schaffner. The research leading to these results has received funding from the European Union’s Horizon 2020 program (ERC grant agreement no. 742985 to J.F.) and the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734. S.T. was supported by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). O.N. was supported by the Ministry of Education, Youth and Sports of the Czech Republic (European Regional Development Fund-Project ‘‘Centre for Experimental Plant Biology’’ no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Pospısil was supported by European Regional Development Fund Project ‘‘Centre for Experimental Plant Biology’’\r\n(no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Petrasek was supported by EU Operational Programme Prague-Competitiveness (no. CZ.2.16/3.1.00/21519). ","status":"public","volume":30,"related_material":{"record":[{"status":"public","id":"8822","relation":"dissertation_contains"}]},"issue":"3","external_id":{"isi":["000511287900018"],"pmid":["31956021"]}},{"publication_identifier":{"issn":["24699950"],"eissn":["24699969"]},"publication_status":"published","publication":"Physical Review B","department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"publisher":"American Physical Society","intvolume":"       101","author":[{"orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan"},{"last_name":"Lopes","first_name":"P. L.S.","full_name":"Lopes, P. L.S."},{"full_name":"Hosur, Pavan","first_name":"Pavan","last_name":"Hosur"},{"last_name":"Gilbert","full_name":"Gilbert, Matthew J.","first_name":"Matthew J."},{"full_name":"Ghaemi, Pouyan","first_name":"Pouyan","last_name":"Ghaemi"}],"date_published":"2020-01-13T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-28T13:11:13Z","abstract":[{"text":"In the superconducting regime of FeTe(1−x)Sex, there exist two types of vortices which are distinguished by the presence or absence of zero-energy states in their core. To understand their origin, we examine the interplay of Zeeman coupling and superconducting pairings in three-dimensional metals with band inversion. Weak Zeeman fields are found to suppress intraorbital spin-singlet pairing, known to localize the states at the ends of the vortices on the surface. On the other hand, an orbital-triplet pairing is shown to be stable against Zeeman interactions, but leads to delocalized zero-energy Majorana modes which extend through the vortex. In contrast, the finite-energy vortex modes remain localized at the vortex ends even when the pairing is of orbital-triplet form. Phenomenologically, this manifests as an observed disappearance of zero-bias peaks within the cores of topological vortices upon an increase of the applied magnetic field. The presence of magnetic impurities in FeTe(1−x)Sex, which are attracted to the vortices, would lead to such Zeeman-induced delocalization of Majorana modes in a fraction of vortices that capture a large enough number of magnetic impurities. Our results provide an explanation for the dichotomy between topological and nontopological vortices recently observed in FeTe(1−x)Sex.","lang":"eng"}],"month":"01","scopus_import":"1","arxiv":1,"article_number":"020504","status":"public","volume":101,"external_id":{"isi":["000506843500001"],"arxiv":["1907.02077"]},"issue":"2","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.02077"}],"year":"2020","date_created":"2020-02-02T23:01:01Z","isi":1,"oa":1,"_id":"7428","day":"13","quality_controlled":"1","article_type":"original","article_processing_charge":"No","type":"journal_article","citation":{"ista":"Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. 2020. Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. 101(2), 020504.","ama":"Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. <i>Physical Review B</i>. 2020;101(2). doi:<a href=\"https://doi.org/10.1103/PhysRevB.101.020504\">10.1103/PhysRevB.101.020504</a>","chicago":"Ghazaryan, Areg, P. L.S. Lopes, Pavan Hosur, Matthew J. Gilbert, and Pouyan Ghaemi. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevB.101.020504\">https://doi.org/10.1103/PhysRevB.101.020504</a>.","short":"A. Ghazaryan, P.L.S. Lopes, P. Hosur, M.J. Gilbert, P. Ghaemi, Physical Review B 101 (2020).","apa":"Ghazaryan, A., Lopes, P. L. S., Hosur, P., Gilbert, M. J., &#38; Ghaemi, P. (2020). Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.101.020504\">https://doi.org/10.1103/PhysRevB.101.020504</a>","mla":"Ghazaryan, Areg, et al. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” <i>Physical Review B</i>, vol. 101, no. 2, 020504, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevB.101.020504\">10.1103/PhysRevB.101.020504</a>.","ieee":"A. Ghazaryan, P. L. S. Lopes, P. Hosur, M. J. Gilbert, and P. Ghaemi, “Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors,” <i>Physical Review B</i>, vol. 101, no. 2. American Physical Society, 2020."},"title":"Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors","doi":"10.1103/PhysRevB.101.020504"},{"publication_identifier":{"eissn":["17425662"]},"publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"EdHa"}],"publication":"Journal of the Royal Society Interface","publisher":"The Royal Society","intvolume":"        17","author":[{"first_name":"Artemy","full_name":"Kolchinsky, Artemy","last_name":"Kolchinsky"},{"full_name":"Corominas-Murtra, Bernat","first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra","orcid":"0000-0001-9806-5643"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-01-29T00:00:00Z","date_updated":"2023-08-17T14:31:28Z","abstract":[{"lang":"eng","text":"In many real-world systems, information can be transmitted in two qualitatively different ways: by copying or by transformation. Copying occurs when messages are transmitted without modification, e.g. when an offspring receives an unaltered copy of a gene from its parent. Transformation occurs when messages are modified systematically during transmission, e.g. when mutational biases occur during genetic replication. Standard information-theoretic measures do not distinguish these two modes of information transfer, although they may reflect different mechanisms and have different functional consequences. Starting from a few simple axioms, we derive a decomposition of mutual information into the information transmitted by copying versus the information transmitted by transformation. We begin with a decomposition that applies when the source and destination of the channel have the same set of messages and a notion of message identity exists. We then generalize our decomposition to other kinds of channels, which can involve different source and destination sets and broader notions of similarity. In addition, we show that copy information can be interpreted as the minimal work needed by a physical copying process, which is relevant for understanding the physics of replication. We use the proposed decomposition to explore a model of amino acid substitution rates. Our results apply to any system in which the fidelity of copying, rather than simple predictability, is of critical relevance."}],"month":"01","scopus_import":"1","article_number":"0623","arxiv":1,"acknowledgement":"AK was supported by Grant No. FQXi-RFP-1622 from the FQXi foundation, and Grant No. CHE-1648973 from the U.S.\r\nNational Science Foundation. AK would like to thank the Santa Fe Institute for supporting this research. The authors\r\nthank Jordi Fortuny, Rudolf Hanel, Joshua Garland, and Blai Vidiella for helpful discussions, as well as the anonymous\r\nreviewers for their insightful suggestions. ","volume":17,"status":"public","external_id":{"pmid":["31964273"],"isi":["000538369800002"],"arxiv":["1903.10693"]},"issue":"162","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1903.10693","open_access":"1"}],"year":"2020","date_created":"2020-02-02T23:01:03Z","isi":1,"oa":1,"_id":"7431","quality_controlled":"1","day":"29","article_processing_charge":"No","article_type":"original","type":"journal_article","citation":{"ista":"Kolchinsky A, Corominas-Murtra B. 2020. Decomposing information into copying versus transformation. Journal of the Royal Society Interface. 17(162), 0623.","chicago":"Kolchinsky, Artemy, and Bernat Corominas-Murtra. “Decomposing Information into Copying versus Transformation.” <i>Journal of the Royal Society Interface</i>. The Royal Society, 2020. <a href=\"https://doi.org/10.1098/rsif.2019.0623\">https://doi.org/10.1098/rsif.2019.0623</a>.","ama":"Kolchinsky A, Corominas-Murtra B. Decomposing information into copying versus transformation. <i>Journal of the Royal Society Interface</i>. 2020;17(162). doi:<a href=\"https://doi.org/10.1098/rsif.2019.0623\">10.1098/rsif.2019.0623</a>","apa":"Kolchinsky, A., &#38; Corominas-Murtra, B. (2020). Decomposing information into copying versus transformation. <i>Journal of the Royal Society Interface</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsif.2019.0623\">https://doi.org/10.1098/rsif.2019.0623</a>","mla":"Kolchinsky, Artemy, and Bernat Corominas-Murtra. “Decomposing Information into Copying versus Transformation.” <i>Journal of the Royal Society Interface</i>, vol. 17, no. 162, 0623, The Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rsif.2019.0623\">10.1098/rsif.2019.0623</a>.","short":"A. Kolchinsky, B. Corominas-Murtra, Journal of the Royal Society Interface 17 (2020).","ieee":"A. Kolchinsky and B. Corominas-Murtra, “Decomposing information into copying versus transformation,” <i>Journal of the Royal Society Interface</i>, vol. 17, no. 162. The Royal Society, 2020."},"title":"Decomposing information into copying versus transformation","doi":"10.1098/rsif.2019.0623","pmid":1},{"oa_version":"Published Version","year":"2020","date_created":"2020-02-06T14:56:53Z","related_material":{"record":[{"status":"public","id":"6608","relation":"part_of_dissertation"}]},"status":"public","supervisor":[{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"}],"article_processing_charge":"No","ddc":["514"],"type":"dissertation","citation":{"ama":"Ölsböck K. The hole system of triangulated shapes. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7460\">10.15479/AT:ISTA:7460</a>","chicago":"Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7460\">https://doi.org/10.15479/AT:ISTA:7460</a>.","ista":"Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria.","apa":"Ölsböck, K. (2020). <i>The hole system of triangulated shapes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7460\">https://doi.org/10.15479/AT:ISTA:7460</a>","mla":"Ölsböck, Katharina. <i>The Hole System of Triangulated Shapes</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7460\">10.15479/AT:ISTA:7460</a>.","short":"K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020.","ieee":"K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science and Technology Austria, 2020."},"title":"The hole system of triangulated shapes","doi":"10.15479/AT:ISTA:7460","oa":1,"_id":"7460","tmp":{"short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png"},"day":"10","publisher":"Institute of Science and Technology Austria","keyword":["shape reconstruction","hole manipulation","ordered complexes","Alpha complex","Wrap complex","computational topology","Bregman geometry"],"degree_awarded":"PhD","author":[{"orcid":"0000-0002-4672-8297","last_name":"Ölsböck","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","first_name":"Katharina","full_name":"Ölsböck, Katharina"}],"has_accepted_license":"1","page":"155","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"month":"02","alternative_title":["ISTA Thesis"],"file_date_updated":"2020-07-14T12:47:58Z","file":[{"creator":"koelsboe","date_created":"2020-02-06T14:43:54Z","access_level":"open_access","content_type":"application/pdf","file_name":"thesis_ist-final_noack.pdf","date_updated":"2020-07-14T12:47:58Z","checksum":"1df9f8c530b443c0e63a3f2e4fde412e","file_id":"7461","relation":"main_file","file_size":76195184},{"creator":"koelsboe","date_created":"2020-02-06T14:52:45Z","access_level":"closed","content_type":"application/x-zip-compressed","description":"latex source files, figures","file_name":"latex-files.zip","date_updated":"2020-07-14T12:47:58Z","checksum":"7a52383c812b0be64d3826546509e5a4","file_id":"7462","relation":"source_file","file_size":122103715}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","date_published":"2020-02-10T00:00:00Z","date_updated":"2023-09-07T13:15:30Z","abstract":[{"lang":"eng","text":"Many methods for the reconstruction of shapes from sets of points produce ordered simplicial complexes, which are collections of vertices, edges, triangles, and their higher-dimensional analogues, called simplices, in which every simplex gets assigned a real value measuring its size. This thesis studies ordered simplicial complexes, with a focus on their topology, which reflects the connectedness of the represented shapes and the presence of holes. We are interested both in understanding better the structure of these complexes, as well as in developing algorithms for applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure for a simplex is the radius of the smallest empty circumsphere. Based on it, we revisit Alpha and Wrap complexes and experimentally determine their probabilistic properties for random data. Also, we prove the existence of tri-partitions, propose algorithms to open and close holes, and extend the concepts from Euclidean to Bregman geometries."}]},{"citation":{"apa":"Dick, R. A., Xu, C., Morado, D. R., Kravchuk, V., Ricana, C. L., Lyddon, T. D., … Schur, F. K. (2020). Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. <i>PLOS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.ppat.1008277\">https://doi.org/10.1371/journal.ppat.1008277</a>","mla":"Dick, Robert A., et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” <i>PLOS Pathogens</i>, vol. 16, no. 1, e1008277, Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.ppat.1008277\">10.1371/journal.ppat.1008277</a>.","short":"R.A. Dick, C. Xu, D.R. Morado, V. Kravchuk, C.L. Ricana, T.D. Lyddon, A.M. Broad, J.R. Feathers, M.C. Johnson, V.M. Vogt, J.R. Perilla, J.A.G. Briggs, F.K. Schur, PLOS Pathogens 16 (2020).","chicago":"Dick, Robert A., Chaoyi Xu, Dustin R. Morado, Vladyslav Kravchuk, Clifton L. Ricana, Terri D. Lyddon, Arianna M. Broad, et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” <i>PLOS Pathogens</i>. Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.ppat.1008277\">https://doi.org/10.1371/journal.ppat.1008277</a>.","ama":"Dick RA, Xu C, Morado DR, et al. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. <i>PLOS Pathogens</i>. 2020;16(1). doi:<a href=\"https://doi.org/10.1371/journal.ppat.1008277\">10.1371/journal.ppat.1008277</a>","ista":"Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FK. 2020. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 16(1), e1008277.","ieee":"R. A. Dick <i>et al.</i>, “Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly,” <i>PLOS Pathogens</i>, vol. 16, no. 1. Public Library of Science, 2020."},"project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF"}],"title":"Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly","pmid":1,"doi":"10.1371/journal.ppat.1008277","article_type":"original","article_processing_charge":"No","type":"journal_article","ddc":["570"],"day":"27","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","oa":1,"_id":"7464","date_created":"2020-02-06T18:47:17Z","isi":1,"oa_version":"Published Version","year":"2020","external_id":{"pmid":["31986188"],"isi":["000510746400010"]},"issue":"1","related_material":{"record":[{"id":"9723","status":"deleted","relation":"research_data"}]},"article_number":"e1008277","volume":16,"status":"public","scopus_import":"1","file_date_updated":"2020-07-14T12:47:59Z","month":"01","abstract":[{"text":"Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly.","lang":"eng"}],"date_updated":"2023-10-17T12:29:34Z","file":[{"date_created":"2020-02-11T10:07:28Z","creator":"dernst","access_level":"open_access","content_type":"application/pdf","file_name":"2020_PLOSPatho_Dick.pdf","file_id":"7484","relation":"main_file","date_updated":"2020-07-14T12:47:59Z","checksum":"a297f54d1fef0efe4789ca00f37f241e","file_size":4551246}],"date_published":"2020-01-27T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"ScienComp"}],"author":[{"first_name":"Robert A.","full_name":"Dick, Robert A.","last_name":"Dick"},{"full_name":"Xu, Chaoyi","first_name":"Chaoyi","last_name":"Xu"},{"last_name":"Morado","first_name":"Dustin R.","full_name":"Morado, Dustin R."},{"last_name":"Kravchuk","first_name":"Vladyslav","full_name":"Kravchuk, Vladyslav","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9523-9089"},{"first_name":"Clifton L.","full_name":"Ricana, Clifton L.","last_name":"Ricana"},{"last_name":"Lyddon","first_name":"Terri D.","full_name":"Lyddon, Terri D."},{"last_name":"Broad","first_name":"Arianna M.","full_name":"Broad, Arianna M."},{"last_name":"Feathers","first_name":"J. Ryan","full_name":"Feathers, J. Ryan"},{"last_name":"Johnson","full_name":"Johnson, Marc C.","first_name":"Marc C."},{"first_name":"Volker M.","full_name":"Vogt, Volker M.","last_name":"Vogt"},{"last_name":"Perilla","full_name":"Perilla, Juan R.","first_name":"Juan R."},{"last_name":"Briggs","first_name":"John A. G.","full_name":"Briggs, John A. G."},{"orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur"}],"has_accepted_license":"1","publisher":"Public Library of Science","intvolume":"        16","publication_status":"published","publication":"PLOS Pathogens","language":[{"iso":"eng"}],"department":[{"_id":"FlSc"}],"publication_identifier":{"issn":["1553-7374"]}},{"status":"public","volume":293,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11626"}]},"article_number":"110414","issue":"4","external_id":{"isi":["000520609800009"]},"year":"2020","oa_version":"Published Version","isi":1,"date_created":"2020-02-09T23:00:50Z","_id":"7465","oa":1,"day":"01","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","ddc":["580"],"article_type":"original","article_processing_charge":"No","title":"Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis","doi":"10.1016/j.plantsci.2020.110414","citation":{"ieee":"E. Mazur, M. C. Gallei, M. Adamowski, H. Han, H. S. Robert, and J. Friml, “Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis,” <i>Plant Science</i>, vol. 293, no. 4. Elsevier, 2020.","ama":"Mazur E, Gallei MC, Adamowski M, Han H, Robert HS, Friml J. Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. <i>Plant Science</i>. 2020;293(4). doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">10.1016/j.plantsci.2020.110414</a>","chicago":"Mazur, Ewa, Michelle C Gallei, Maciek Adamowski, Huibin Han, Hélène S. Robert, and Jiří Friml. “Clathrin-Mediated Trafficking and PIN Trafficking Are Required for Auxin Canalization and Vascular Tissue Formation in Arabidopsis.” <i>Plant Science</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">https://doi.org/10.1016/j.plantsci.2020.110414</a>.","ista":"Mazur E, Gallei MC, Adamowski M, Han H, Robert HS, Friml J. 2020. Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. Plant Science. 293(4), 110414.","short":"E. Mazur, M.C. Gallei, M. Adamowski, H. Han, H.S. Robert, J. Friml, Plant Science 293 (2020).","apa":"Mazur, E., Gallei, M. C., Adamowski, M., Han, H., Robert, H. S., &#38; Friml, J. (2020). Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. <i>Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">https://doi.org/10.1016/j.plantsci.2020.110414</a>","mla":"Mazur, Ewa, et al. “Clathrin-Mediated Trafficking and PIN Trafficking Are Required for Auxin Canalization and Vascular Tissue Formation in Arabidopsis.” <i>Plant Science</i>, vol. 293, no. 4, 110414, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">10.1016/j.plantsci.2020.110414</a>."},"project":[{"call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["01689452"],"eissn":["18732259"]},"ec_funded":1,"publication":"Plant Science","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"publication_status":"published","intvolume":"       293","publisher":"Elsevier","has_accepted_license":"1","author":[{"last_name":"Mazur","first_name":"Ewa","full_name":"Mazur, Ewa"},{"last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C","first_name":"Michelle C","orcid":"0000-0003-1286-7368"},{"orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","full_name":"Adamowski, Maciek","last_name":"Adamowski"},{"last_name":"Han","full_name":"Han, Huibin","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hélène S.","full_name":"Robert, Hélène S.","last_name":"Robert"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"date_published":"2020-04-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"relation":"main_file","file_id":"7471","checksum":"f7f27c6a8fea985ceb9279be2204461c","date_updated":"2020-07-14T12:47:59Z","file_size":3499069,"date_created":"2020-02-10T08:59:36Z","creator":"dernst","content_type":"application/pdf","file_name":"2020_PlantScience_Mazur.pdf","access_level":"open_access"}],"abstract":[{"text":"The flexible development of plants is characterized by a high capacity for post-embryonic organ formation and tissue regeneration, processes, which require tightly regulated intercellular communication and coordinated tissue (re-)polarization. The phytohormone auxin, the main driver for these processes, is able to establish polarized auxin transport channels, which are characterized by the expression and polar, subcellular localization of the PIN1 auxin transport proteins. These channels are demarcating the position of future vascular strands necessary for organ formation and tissue regeneration. Major progress has been made in the last years to understand how PINs can change their polarity in different contexts and thus guide auxin flow through the plant. However, it still remains elusive how auxin mediates the establishment of auxin conducting channels and the formation of vascular tissue and which cellular processes are involved. By the means of sophisticated regeneration experiments combined with local auxin applications in Arabidopsis thaliana inflorescence stems we show that (i) PIN subcellular dynamics, (ii) PIN internalization by clathrin-mediated trafficking and (iii) an intact actin cytoskeleton required for post-endocytic trafficking are indispensable for auxin channel formation, de novo vascular formation and vascular regeneration after wounding. These observations provide novel insights into cellular mechanism of coordinated tissue polarization during auxin canalization.","lang":"eng"}],"date_updated":"2023-08-17T14:37:32Z","month":"04","scopus_import":"1","file_date_updated":"2020-07-14T12:47:59Z"},{"author":[{"first_name":"Katrin","full_name":"Kierdorf, Katrin","last_name":"Kierdorf"},{"first_name":"Fabian","full_name":"Hersperger, Fabian","last_name":"Hersperger"},{"last_name":"Sharrock","full_name":"Sharrock, Jessica","first_name":"Jessica"},{"last_name":"Vincent","first_name":"Crystal M.","full_name":"Vincent, Crystal M."},{"last_name":"Ustaoglu","first_name":"Pinar","full_name":"Ustaoglu, Pinar"},{"last_name":"Dou","first_name":"Jiawen","full_name":"Dou, Jiawen"},{"orcid":"0000-0002-1819-198X","first_name":"Attila","full_name":"György, Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","last_name":"György"},{"last_name":"Groß","first_name":"Olaf","full_name":"Groß, Olaf"},{"orcid":"0000-0001-8323-8353","first_name":"Daria E","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus"},{"first_name":"Marc S.","full_name":"Dionne, Marc S.","last_name":"Dionne"}],"has_accepted_license":"1","publisher":"eLife Sciences Publications","intvolume":"         9","publication_status":"published","publication":"eLife","department":[{"_id":"DaSi"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2050084X"]},"scopus_import":"1","file_date_updated":"2020-07-14T12:47:59Z","month":"01","abstract":[{"text":"Unpaired ligands are secreted signals that act via a GP130-like receptor, domeless, to activate JAK/STAT signalling in Drosophila. Like many mammalian cytokines, unpaireds can be activated by infection and other stresses and can promote insulin resistance in target tissues. However, the importance of this effect in non-inflammatory physiology is unknown. Here, we identify a requirement for unpaired-JAK signalling as a metabolic regulator in healthy adult Drosophila muscle. Adult muscles show basal JAK-STAT signalling activity in the absence of any immune challenge. Plasmatocytes (Drosophila macrophages) are an important source of this tonic signal. Loss of the dome receptor on adult muscles significantly reduces lifespan and causes local and systemic metabolic pathology. These pathologies result from hyperactivation of AKT and consequent deregulation of metabolism. Thus, we identify a cytokine signal that must be received in muscle to control AKT activity and metabolic homeostasis.","lang":"eng"}],"date_updated":"2023-08-17T14:36:39Z","file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"2020_eLife_Kierdorf.pdf","creator":"dernst","date_created":"2020-02-10T08:53:16Z","file_size":4959933,"date_updated":"2020-07-14T12:47:59Z","checksum":"3a072be843f416c7a7d532a51dc0addb","file_id":"7470","relation":"main_file"}],"date_published":"2020-01-20T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2020-02-09T23:00:51Z","isi":1,"oa_version":"Published Version","year":"2020","external_id":{"isi":["000512304800001"]},"article_number":"e51595","status":"public","volume":9,"citation":{"ieee":"K. Kierdorf <i>et al.</i>, “Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","short":"K. Kierdorf, F. Hersperger, J. Sharrock, C.M. Vincent, P. Ustaoglu, J. Dou, A. György, O. Groß, D.E. Siekhaus, M.S. Dionne, ELife 9 (2020).","mla":"Kierdorf, Katrin, et al. “Muscle Function and Homeostasis Require Cytokine Inhibition of AKT Activity in Drosophila.” <i>ELife</i>, vol. 9, e51595, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.51595\">10.7554/eLife.51595</a>.","apa":"Kierdorf, K., Hersperger, F., Sharrock, J., Vincent, C. M., Ustaoglu, P., Dou, J., … Dionne, M. S. (2020). Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.51595\">https://doi.org/10.7554/eLife.51595</a>","ista":"Kierdorf K, Hersperger F, Sharrock J, Vincent CM, Ustaoglu P, Dou J, György A, Groß O, Siekhaus DE, Dionne MS. 2020. Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. eLife. 9, e51595.","chicago":"Kierdorf, Katrin, Fabian Hersperger, Jessica Sharrock, Crystal M. Vincent, Pinar Ustaoglu, Jiawen Dou, Attila György, Olaf Groß, Daria E Siekhaus, and Marc S. Dionne. “Muscle Function and Homeostasis Require Cytokine Inhibition of AKT Activity in Drosophila.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.51595\">https://doi.org/10.7554/eLife.51595</a>.","ama":"Kierdorf K, Hersperger F, Sharrock J, et al. Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.51595\">10.7554/eLife.51595</a>"},"project":[{"name":"Drosophila TNFa´s Funktion in Immunzellen","grant_number":"P29638","call_identifier":"FWF","_id":"253B6E48-B435-11E9-9278-68D0E5697425"}],"doi":"10.7554/eLife.51595","title":"Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila","article_type":"original","article_processing_charge":"No","ddc":["570"],"type":"journal_article","day":"20","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","oa":1,"_id":"7466"},{"month":"03","file_date_updated":"2022-08-23T08:34:17Z","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-03-01T00:00:00Z","file":[{"checksum":"f23be731a766a480c77c962c1380315c","date_updated":"2022-08-23T08:34:17Z","relation":"main_file","file_id":"11942","file_size":6423548,"success":1,"creator":"dernst","date_created":"2022-08-23T08:34:17Z","content_type":"application/pdf","file_name":"2020_ACSAppliedEnergyMat_Cadavid.pdf","access_level":"open_access"}],"date_updated":"2023-08-17T14:36:16Z","abstract":[{"text":"Nanomaterials produced from the bottom-up assembly of nanocrystals may incorporate ∼1020–1021 cm–3 not fully coordinated surface atoms, i.e., ∼1020–1021 cm–3 potential donor or acceptor states that can strongly affect transport properties. Therefore, to exploit the full potential of nanocrystal building blocks to produce functional nanomaterials and thin films, a proper control of their surface chemistry is required. Here, we analyze how the ligand stripping procedure influences the charge and heat transport properties of sintered PbSe nanomaterials produced from the bottom-up assembly of colloidal PbSe nanocrystals. First, we show that the removal of the native organic ligands by thermal decomposition in an inert atmosphere leaves relatively large amounts of carbon at the crystal interfaces. This carbon blocks crystal growth during consolidation and at the same time hampers charge and heat transport through the final nanomaterial. Second, we demonstrate that, by stripping ligands from the nanocrystal surface before consolidation, nanomaterials with larger crystal domains, lower porosity, and higher charge carrier concentrations are obtained, thus resulting in nanomaterials with higher electrical and thermal conductivities. In addition, the ligand displacement leaves the nanocrystal surface unprotected, facilitating oxidation and chalcogen evaporation. The influence of the ligand displacement on the nanomaterial charge transport properties is rationalized here using a two-band model based on the standard Boltzmann transport equation with the relaxation time approximation. Finally, we present an application of the produced functional nanomaterials by modeling, fabricating, and testing a simple PbSe-based thermoelectric device with a ring geometry.","lang":"eng"}],"intvolume":"         3","publisher":"American Chemical Society","has_accepted_license":"1","author":[{"last_name":"Cadavid","full_name":"Cadavid, Doris","first_name":"Doris"},{"last_name":"Ortega","full_name":"Ortega, Silvia","first_name":"Silvia"},{"last_name":"Illera","full_name":"Illera, Sergio","first_name":"Sergio"},{"id":"2A70014E-F248-11E8-B48F-1D18A9856A87","first_name":"Yu","full_name":"Liu, Yu","last_name":"Liu","orcid":"0000-0001-7313-6740"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Ibáñez, Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843"},{"full_name":"Shavel, Alexey","first_name":"Alexey","last_name":"Shavel"},{"first_name":"Yu","full_name":"Zhang, Yu","last_name":"Zhang"},{"last_name":"Li","first_name":"Mengyao","full_name":"Li, Mengyao"},{"last_name":"López","full_name":"López, Antonio M.","first_name":"Antonio M."},{"last_name":"Noriega","first_name":"Germán","full_name":"Noriega, Germán"},{"last_name":"Durá","full_name":"Durá, Oscar Juan","first_name":"Oscar Juan"},{"last_name":"López De La Torre","first_name":"M. A.","full_name":"López De La Torre, M. A."},{"last_name":"Prades","full_name":"Prades, Joan Daniel","first_name":"Joan Daniel"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"}],"publication_identifier":{"eissn":["2574-0962"]},"ec_funded":1,"page":"2120-2129","department":[{"_id":"MaIb"}],"language":[{"iso":"eng"}],"publication":"ACS Applied Energy Materials","publication_status":"published","ddc":["540"],"type":"journal_article","article_processing_charge":"No","article_type":"original","doi":"10.1021/acsaem.9b02137","title":"Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"citation":{"ieee":"D. Cadavid <i>et al.</i>, “Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials,” <i>ACS Applied Energy Materials</i>, vol. 3, no. 3. American Chemical Society, pp. 2120–2129, 2020.","apa":"Cadavid, D., Ortega, S., Illera, S., Liu, Y., Ibáñez, M., Shavel, A., … Cabot, A. (2020). Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. <i>ACS Applied Energy Materials</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsaem.9b02137\">https://doi.org/10.1021/acsaem.9b02137</a>","mla":"Cadavid, Doris, et al. “Influence of the Ligand Stripping on the Transport Properties of Nanoparticle-Based PbSe Nanomaterials.” <i>ACS Applied Energy Materials</i>, vol. 3, no. 3, American Chemical Society, 2020, pp. 2120–29, doi:<a href=\"https://doi.org/10.1021/acsaem.9b02137\">10.1021/acsaem.9b02137</a>.","short":"D. Cadavid, S. Ortega, S. Illera, Y. Liu, M. Ibáñez, A. Shavel, Y. Zhang, M. Li, A.M. López, G. Noriega, O.J. Durá, M.A. López De La Torre, J.D. Prades, A. Cabot, ACS Applied Energy Materials 3 (2020) 2120–2129.","chicago":"Cadavid, Doris, Silvia Ortega, Sergio Illera, Yu Liu, Maria Ibáñez, Alexey Shavel, Yu Zhang, et al. “Influence of the Ligand Stripping on the Transport Properties of Nanoparticle-Based PbSe Nanomaterials.” <i>ACS Applied Energy Materials</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acsaem.9b02137\">https://doi.org/10.1021/acsaem.9b02137</a>.","ista":"Cadavid D, Ortega S, Illera S, Liu Y, Ibáñez M, Shavel A, Zhang Y, Li M, López AM, Noriega G, Durá OJ, López De La Torre MA, Prades JD, Cabot A. 2020. Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. ACS Applied Energy Materials. 3(3), 2120–2129.","ama":"Cadavid D, Ortega S, Illera S, et al. Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. <i>ACS Applied Energy Materials</i>. 2020;3(3):2120-2129. doi:<a href=\"https://doi.org/10.1021/acsaem.9b02137\">10.1021/acsaem.9b02137</a>"},"_id":"7467","oa":1,"quality_controlled":"1","day":"01","year":"2020","oa_version":"Submitted Version","isi":1,"date_created":"2020-02-09T23:00:52Z","acknowledgement":"This work was supported by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP (ENE2016-77798-C4-3-R) and the Generalitat de Catalunya through the project 2017SGR1246. D.C. acknowledges support from Universidad Nacional de Colombia. Y.L. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 754411. M.I. acknowledges financial support from IST Austria.","volume":3,"status":"public","issue":"3","external_id":{"isi":["000526598300012"]}},{"project":[{"_id":"257BBB4C-B435-11E9-9278-68D0E5697425","grant_number":"607616","name":"Inter-and intracellular signalling in schizophrenia","call_identifier":"FP7"}],"citation":{"ista":"Käfer K, Nardin M, Blahna K, Csicsvari JL. 2020. Replay of behavioral sequences in the medial prefrontal cortex during rule switching. Neuron. 106(1), P154–165.e6.","chicago":"Käfer, Karola, Michele Nardin, Karel Blahna, and Jozsef L Csicsvari. “Replay of Behavioral Sequences in the Medial Prefrontal Cortex during Rule Switching.” <i>Neuron</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2020.01.015\">https://doi.org/10.1016/j.neuron.2020.01.015</a>.","ama":"Käfer K, Nardin M, Blahna K, Csicsvari JL. Replay of behavioral sequences in the medial prefrontal cortex during rule switching. <i>Neuron</i>. 2020;106(1):P154-165.e6. doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.01.015\">10.1016/j.neuron.2020.01.015</a>","apa":"Käfer, K., Nardin, M., Blahna, K., &#38; Csicsvari, J. L. (2020). Replay of behavioral sequences in the medial prefrontal cortex during rule switching. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2020.01.015\">https://doi.org/10.1016/j.neuron.2020.01.015</a>","mla":"Käfer, Karola, et al. “Replay of Behavioral Sequences in the Medial Prefrontal Cortex during Rule Switching.” <i>Neuron</i>, vol. 106, no. 1, Elsevier, 2020, p. P154–165.e6, doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.01.015\">10.1016/j.neuron.2020.01.015</a>.","short":"K. Käfer, M. Nardin, K. Blahna, J.L. Csicsvari, Neuron 106 (2020) P154–165.e6.","ieee":"K. Käfer, M. Nardin, K. Blahna, and J. L. Csicsvari, “Replay of behavioral sequences in the medial prefrontal cortex during rule switching,” <i>Neuron</i>, vol. 106, no. 1. Elsevier, p. P154–165.e6, 2020."},"pmid":1,"doi":"10.1016/j.neuron.2020.01.015","title":"Replay of behavioral sequences in the medial prefrontal cortex during rule switching","article_processing_charge":"No","article_type":"original","type":"journal_article","quality_controlled":"1","day":"08","oa":1,"_id":"7472","date_created":"2020-02-10T15:45:48Z","isi":1,"oa_version":"Published Version","year":"2020","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2020.01.015","open_access":"1"}],"external_id":{"pmid":["32032512"],"isi":["000525319300016"]},"issue":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/this-brain-area-helps-us-decide/","relation":"press_release","description":"News on IST Homepage"}]},"acknowledgement":"We thank Todor Asenov and Thomas Menner from the Machine Shop for the drive design and production, Hugo Malagon-Vina for assistance in maze automatization, Jago Wallenschus for taking the images of the histology, and Federico Stella and Juan Felipe Ramirez-Villegas for comments on an earlier version of the manuscript. This work was supported by the EU-FP7 MC-ITN IN-SENS (grant 607616 ).","volume":106,"status":"public","scopus_import":"1","month":"04","abstract":[{"lang":"eng","text":"Temporally organized reactivation of experiences during awake immobility periods is thought to underlie cognitive processes like planning and evaluation. While replay of trajectories is well established for the hippocampus, it is unclear whether the medial prefrontal cortex (mPFC) can reactivate sequential behavioral experiences in the awake state to support task execution. We simultaneously recorded from hippocampal and mPFC principal neurons in rats performing a mPFC-dependent rule-switching task on a plus maze. We found that mPFC neuronal activity encoded relative positions between the start and goal. During awake immobility periods, the mPFC replayed temporally organized sequences of these generalized positions, resembling entire spatial trajectories. The occurrence of mPFC trajectory replay positively correlated with rule-switching performance. However, hippocampal and mPFC trajectory replay occurred independently, indicating different functions. These results demonstrate that the mPFC can replay ordered activity patterns representing generalized locations and suggest that mPFC replay might have a role in flexible behavior."}],"date_updated":"2023-08-17T14:38:02Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-04-08T00:00:00Z","acknowledged_ssus":[{"_id":"M-Shop"}],"author":[{"last_name":"Käfer","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","full_name":"Käfer, Karola","first_name":"Karola"},{"orcid":"0000-0001-8849-6570","last_name":"Nardin","full_name":"Nardin, Michele","first_name":"Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Blahna","id":"3EA859AE-F248-11E8-B48F-1D18A9856A87","first_name":"Karel","full_name":"Blahna, Karel"},{"orcid":"0000-0002-5193-4036","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari"}],"publisher":"Elsevier","intvolume":"       106","publication_status":"published","department":[{"_id":"JoCs"}],"language":[{"iso":"eng"}],"publication":"Neuron","page":"P154-165.e6","ec_funded":1,"publication_identifier":{"issn":["0896-6273"]}},{"isi":1,"date_created":"2020-02-10T15:59:45Z","year":"2020","oa_version":"Published Version","external_id":{"pmid":["31928842"],"isi":["000520854700008"]},"acknowledgement":"This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement No. 692692 and Marie Sklodowska-Curie 708497) and from Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27 Wittgenstein award and DK W1205-B09). We thank Johann Danzl and Ryuichi Shigemoto for critically reading the manuscript; Walter Kaufmann, Daniel Gutl, and Vanessa Zheden for extensive EM training, advice, and experimental assistance; Benjamin Suter for substantial help with light stimulation, ImageJ plugins for analysis, and manuscript editing; Florian Marr and Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; Julia König and Paul Wurzinger (Leica Microsystems) for helpful technical discussions; and Taija Makinen for providing the Prox1-CreERT2 mouse line.","status":"public","volume":105,"related_material":{"record":[{"relation":"dissertation_contains","id":"11196","status":"public"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/flash-and-freeze-reveals-dynamics-of-nerve-connections/","relation":"press_release"}]},"doi":"10.1016/j.neuron.2019.12.022","pmid":1,"title":"Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"708497","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Zellkommunikation in Gesundheit und Krankheit","grant_number":"W01205"}],"citation":{"apa":"Borges Merjane, C., Kim, O., &#38; Jonas, P. M. (2020). Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2019.12.022\">https://doi.org/10.1016/j.neuron.2019.12.022</a>","mla":"Borges Merjane, Carolina, et al. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” <i>Neuron</i>, vol. 105, Elsevier, 2020, pp. 992–1006, doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.12.022\">10.1016/j.neuron.2019.12.022</a>.","short":"C. Borges Merjane, O. Kim, P.M. Jonas, Neuron 105 (2020) 992–1006.","ama":"Borges Merjane C, Kim O, Jonas PM. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. <i>Neuron</i>. 2020;105:992-1006. doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.12.022\">10.1016/j.neuron.2019.12.022</a>","ista":"Borges Merjane C, Kim O, Jonas PM. 2020. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. 105, 992–1006.","chicago":"Borges Merjane, Carolina, Olena Kim, and Peter M Jonas. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” <i>Neuron</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2019.12.022\">https://doi.org/10.1016/j.neuron.2019.12.022</a>.","ieee":"C. Borges Merjane, O. Kim, and P. M. Jonas, “Functional electron microscopy (‘Flash and Freeze’) of identified cortical synapses in acute brain slices,” <i>Neuron</i>, vol. 105. Elsevier, pp. 992–1006, 2020."},"type":"journal_article","ddc":["570"],"article_processing_charge":"No","article_type":"original","quality_controlled":"1","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"day":"18","_id":"7473","oa":1,"has_accepted_license":"1","author":[{"orcid":"0000-0003-0005-401X","first_name":"Carolina","full_name":"Borges Merjane, Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87","last_name":"Borges Merjane"},{"id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","full_name":"Kim, Olena","first_name":"Olena","last_name":"Kim"},{"orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","first_name":"Peter M"}],"intvolume":"       105","publisher":"Elsevier","language":[{"iso":"eng"}],"department":[{"_id":"PeJo"}],"publication":"Neuron","publication_status":"published","publication_identifier":{"issn":["0896-6273"]},"ec_funded":1,"page":"992-1006","file_date_updated":"2020-11-20T08:58:53Z","scopus_import":"1","month":"03","abstract":[{"lang":"eng","text":"How structural and functional properties of synapses relate to each other is a fundamental question in neuroscience. Electrophysiology has elucidated mechanisms of synaptic transmission, and electron microscopy (EM) has provided insight into morphological properties of synapses. Here we describe an enhanced method for functional EM (“flash and freeze”), combining optogenetic stimulation with high-pressure freezing. We demonstrate that the improved method can be applied to intact networks in acute brain slices and organotypic slice cultures from mice. As a proof of concept, we probed vesicle pool changes during synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapse. Our findings show overlap of the docked vesicle pool and the functionally defined readily releasable pool and provide evidence of fast endocytosis at this synapse. Functional EM with acute slices and slice cultures has the potential to reveal the structural and functional mechanisms of transmission in intact, genetically perturbed, and disease-affected synapses."}],"date_updated":"2024-03-25T23:30:04Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-03-18T00:00:00Z","file":[{"creator":"dernst","success":1,"date_created":"2020-11-20T08:58:53Z","access_level":"open_access","content_type":"application/pdf","file_name":"2020_Neuron_BorgesMerjane.pdf","date_updated":"2020-11-20T08:58:53Z","checksum":"3582664addf26859e86ac5bec3e01416","file_id":"8778","relation":"main_file","file_size":9712957}]}]